Bacterial artificial chromosome (BAC) libraries are still a valuable tool for de novo assembly of complex genomes, such as many plants genomes. Shotgun sequencing of BACs, individually or by pools, produces first assemblies which usually need further improvement towards finished quality. We developed a new approach to obtain BAC ends libraries for Illumina sequencing (BES), overcoming the expensive and time consuming BAC ends Sanger sequencing. This new method could be useful for improving de novo assembly, especially in the case of highly repeated genomes.